Team:Madrid-OLM/Computationaimprovement
Computational improvement of the aptamer
The target of this protocol is to improve the union affinity between the protein and the aptamer, obtained by the process that had been explained previously, by bioinformatics methods.
To carry out this affinity improvement, you can start from only 2 elements: the DNA aptamer sequence and the name or preferably the amino acid protein sequence. However, any extra information that you could find in previous studies could be so helpful to save time and reduce the margin of cumulative error. The complete protocol have four different sections:
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• Obtaining the 3D protein structure.
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• Obtaining the 3D aptamer structure (most critical point).
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• Search of the binding site between protein and aptamer through a docking process.
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• Study of the union and proposal of mutation in the sequence.
It is very important to understand that this process not guarantee a better result. However it gives the opportunity of improve the aptamer obtained. Although there are so much works with proteins structures and the interaction between each other’s, there are almost no studies that work with nucleic acids in simulation or structure prediction terms beyond double strand helix. Therefore any final result obtained should be checked in the laboratory, either to confirm or discard the new sequence obtained.
Obtaining the 3D protein structure
The final result of this sección should be a file in .pdb format where we can find the coordinates of every single atom of the protein. That file could be interpreted by bioinformatics programs like Phymol or Chimera and represent the protein in different graphical ways. To obtain it, there are two different paths depending on one fact: has the protein been previously crystallographed?
A structure obtained experimentally exists
We will simply use this proven structure. This will be the most reliable method due to it has been the result of a group's investigation. To check if there is any previous structure we recommend the following simple steps:
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1. Access the UniProt server and search for the protein of interest.
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2. Search for the structure description area and check if it has an entry to the Protein Data Bank (PDB) database.
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3. In the positive case, access that PDB entry and download the file that is needed.
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4. In case of no entry, the steps explained in the next section must be performed.
Clarification, the PDB is a universal database where are the 3D structure of all proteins which have been obtained its structure experimentally. That is, any structure that we find there is quite reliable and proven. However, predictions of structures are not included, owing to this procedure is not experimental.
A structure obtained experimentally don’t exists.
Obtaining the 3D protein structure
Cosas del apartado 1, se necesita meter mas divs seguramente
Obtaining the 3D protein structure
Cosas del apartado 1, se necesita meter mas divs seguramente
Obtaining the 3D protein structure
Cosas del apartado 1, se necesita meter mas divs seguramente